chr6-11017592-A-G

Variant names:

• chr6-11017592-A-G
• rs1570069
• NM_017770.4:c.4-6783T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017770.4(ELOVL2):​c.4-6783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,022 control chromosomes in the GnomAD database, including 23,680 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23680 hom., cov: 32)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 10 publications found

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017770.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	NM_017770.4	MANE Select	c.4-6783T>C		intron	N/A	NP_060240.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	ENST00000354666.4	TSL:1 MANE Select	c.4-6783T>C		intron	N/A	ENSP00000346693.3	Q9NXB9
	ELOVL2	ENST00000854794.1		c.4-6783T>C		intron	N/A	ENSP00000524853.1
	ELOVL2	ENST00000854793.1		c.4-6783T>C		intron	N/A	ENSP00000524852.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82643 AN: 151904 Hom.: 23635 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.544 AC: 82746 AN: 152022 Hom.: 23680 Cov.: 32 AF XY: 0.551 AC XY: 40945 AN XY: 74314

African (AFR) AF: 0.648 AC: 26871 AN: 41458

American (AMR) AF: 0.638 AC: 9734 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4677 AN: 5168

South Asian (SAS) AF: 0.663 AC: 3193 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5064 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29665 AN: 67966

Other (OTH) AF: 0.537 AC: 1133 AN: 2110

Alfa AF: 0.492 Hom.: 16199

Bravo AF: 0.561

Asia WGS AF: 0.754 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.62
DANN	Benign	0.86
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1570069; hg19: chr6-11017825;